MolNFT v1 · #34185 · protein
Crystal structure of unsaturated rhamnogalacturonyl hydrolase in complex with dglca-galnac
2D8L · Putative glycosyl hydrolase yter: “Crystal structure of unsaturated rhamnogalacturonyl hydrolase in complex with dglca-galnac”. X-ray diffraction, 2 ligands (GCD, NGA), 2 pockets (best druggability 0.59). MolNFT v1 #34185 on…
- PDB
- 2D8L
- Type
- protein
- Length
- 363 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycosyl hydrolase yter
- EC
- 3.2.1.-
- UniProt
- O34559
- Ligands
- GCD, NGA
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glycosyl hydrolase yter (EC 3.2.1.-) | protein | 363 | 57% helix, 7% strand | O34559 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.59 | 0.81 | 27 | empty |
| 2 | 56 | 0.35 | 0.79 | 14 | GCD |
Compared structures
- 2D8L · Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc · the same entry in another collection · chain A against A, TM-score 1.00
- O34559 · AlphaFold monomer V2.0 prediction for unsaturated rhamnogalacturonyl hydrolase yter… · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O34559
- Elsewhere: RCSB PDB 2D8L · PDBe 2D8L · UniProt O34559
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.